Refit only replenishes your ammo stores and fuel load. You cannot choose fuel-only or ammo-only. Everything is topped up. This action is instantaneous. It's like a drive-thru for subs.
'End Patrol' will replenish ammo AND fix your boat but it will use up a few weeks of sim-time. If you haven't met the objectives of the mission, no problem.. just reselect it and resume. Your previous success will be carried over.
When you choose to refit or end patrol is up to you. Other than the lost time sailing back to port, there is no penalty. Keep in mind that hull damage will reduce your crush depth so be careful. (in one of my patrols, damage was so bad, I could barely get to periscope depth without flooding.)
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../Dan/..
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